KO_enrich {ReporterScore}

Perform enrichment analysis

Description

This function performs KO enrichment analysis using the 'clusterProfiler' package.

Usage

KO_enrich(
  ko_stat,
  padj_threshold = 0.05,
  logFC_threshold = NULL,
  add_mini = NULL,
  p.adjust.method = "BH",
  type = c("pathway", "module")[1],
  feature = "ko",
  modulelist = NULL,
  verbose = TRUE
)

as.enrich_res(gsea_res)

Arguments

ko_stat

ko_stat dataframe from ko.test.

padj_threshold

p.adjust threshold to determine whether a feature significant or not. p.adjust < padj_threshold, default: 0.05

logFC_threshold

logFC threshold to determine whether a feature significant or not. abs(logFC)>logFC_threshold, default: NULL

add_mini

add_mini when calculate the logFC. e.g (10+0.1)/(0+0.1), default 0.05*min(avg_abundance)

p.adjust.method

The method used for p-value adjustment (default: "BH").

type

"pathway" or "module" for default KOlist_file.

feature

one of "ko", "gene", "compound"

modulelist

NULL or customized modulelist dataframe, must contain "id","K_num","KOs","Description" columns. Take the 'KOlist' as example, use custom_modulelist.

verbose

logical

gsea_res

gsea_res from KO_gsea

Value

A data frame containing the enrichment results.

enrich_res object

See Also

Other common_enrich: KO_fisher(), KO_gsa(), KO_gsea(), KO_gsva(), KO_padog(), KO_safe(), KO_sea(), plot_enrich_res()

Examples

## use `enricher` from the `clusterProfiler` package.
if (requireNamespace("clusterProfiler")) {
  data("reporter_score_res")
  enrich_res <- KO_enrich(reporter_score_res)
  plot(enrich_res)
}